Welcome to the ESID 2022 Meeting Interactive Programme

Background and Aims

Common variable immunodeficiency (CVID) is a heterogeneous disease with various clinical presentations. Currently, less than 20% of cases of CVID have a known genetic cause, considered as monogenic but not following a mendelian inheritance pattern in most of the cases. More complex genetic scenarios like oligogenic inheritance must be considered.

ORVAL, Oligogenic Resource for Variant AnaLysis, is a novel bioinformatics platform designed for the prediction and exploration of candidate disease-causing oligogenic variant combinations.

This study aim to unravel networks of candidate pathogenic variants combinations in a cohort of CVID patients.

Methods

This retrospective study included 35 CVID patients for whom clinical exome sequencing did not disclose a monogenic cause.

Clinical exome data of the 35 subjects and of 1536 controls were analysed through ORVAL, focusing on 479 genes associated with immune disorders. Combinations found in at least 2 CVID patients where selected as potential candidate pathogenic variant combinations if not found in controls.

Results

Variant combinations predicted to be pathogenic were statistically significantly higher among CVID patients compared to controls. 3 unrelated couples of patients shared the same multiple combinations considered as pathogenic. None of these combinations were found in the control cohort.

Clinical and B cells phenotype similarities were found in each couple of patients with the same candidate disease-cause associations.

Conclusions

ORVAL platform is a promising tool to address the oligogenic nature of CVID. Our results need to be replicated in an independent cohort of cases and controls. Real impact of these variant combinations at a molecular level needs further confirmation.

Background and Aims

BACKGROUND:

Primary Immunodeficiencies (PIDs) are monogenic disorders of the immune system. Phenotypic variability of PIDs provide challenges studying and clinically managing these inborn errors. Recent studies indicate that up to 10% of autosomal genes randomly commit to expression of a single allele, termed monoallelic expression (MAE). Unlike X-inactivation or imprinting, MAE of genes is not specific to gene clusters or a single chromosome and leads to a diverse population of cells at the transcript level. Despite an increase in the understanding of MAE, both the functional and mechanistic impact in disease is unknown.

AIM:

Identify the contribution of monoallelic expression to the phenotypic variability of primary immunodeficiencies.

Methods

METHODS:

Single T cells were sorted from healthy donor PBMCS (n=6) and expanded into monoclonal populations (n=57). Genomic DNA was isolated from donors for WES and 431 PID genes were examined for exonic heterozygous SNPs. Bulk RNA-seq of the clonal populations was used to determine allele specific expression of PID genes.

Results

RESULTS:

WES identified 172 PID genes with heterozygous SNPs from the 6 donors. RNA-seq data from 18 clones in 4 donors identified 15 PID genes that display allelic bias. While MAE occurs in 7 of the assessed PID genes.

Conclusions

CONCLUSIONS:

Using this system of monoclonal T cell populations, 7 genes which cause primary immunodeficiencies were found to be regulated by monoalllelic expression. Almost all the identified genes have reports of incomplete penetrance. Mutations in 3 of these genes are known to cause autosomal dominant inherited disease, facilitating further study in patient samples.

Background and Aims

Chronic Mucocutaneous Candidiasis (CMC) is a condition characterized by recurrent or persistent infections of the nails, skin, oral and genital mucosa caused by Candida albicans. CMC disease (CMCD) refers to patients with CMC as the predominant clinical phenotype without the other significant clinical manifestations. Autosomal recessive (AR) IL-17RC deficiency is a rare CMCD, with only three cases reported so far. Now, there is no in vitro functional evaluation system for the pathogenicity of IL17RC mutations and that makes a diagnosis difficult.

Methods

We herein studied a Japanese girl with IL-17RC deficiency who suffered from CMCD. We developed a new in vitro system for functional validation of IL17RC mutations and confirmed her genetic pathogenicity as IL-17RC deficiency.

Results

The patient is a seven-year-old Japanese girl who has developed early-onset oral and cutaneous candidiasis from the age of three months. She had no episodes with a susceptibility to other pathogens. Her clinical phenotype thus clearly showed CMCD. Genetic testing identified a novel homozygous IL17RC duplication (Chr3: 9,971,476-9,971,606 dup(+131bp)). This duplication caused a premature stop codon by frameshift, producing a truncated IL-17RC protein. Our new evaluation system based on IL17RC knockout HeLa cells revealed this duplication mutation was loss-of-function, while polymorphisms, for which homozygotes was reported in general population, were validated as isomorphic. The patient’s fibroblasts did not respond to IL-17A, which was restored by introducing WT IL17RC, suggesting that identified mutation caused patient’s clinical phenotype.

Conclusions

Our new evaluation system for IL17RC mutations was accurate and can be useful for the diagnosis of IL-17RC deficiency.

Background and Aims

Heterozygous deletions in TNFAIP3 cause childhood-onset inflammatory disease, which was thought to be completely penetrant before adulthood. The p.I207L polymorphism is globally rare, but has been adaptively introgressed from ancestral Denisovan Hominins to high prevalence in Oceanian populations.

Methods

Patients with TNFAIP3 deletions were identified from a cohort with paediatric autoimmune disease. IkB-dependent phosphorylation and activation of A20 was assessed in patient cells and cell lines containing p.I207L and other polymorphic TNFAIP3 variants. CRISPR/Cas9 gene-edited mice possessed either a TNFAIP3 deletion, the I207L variant, or both, and were exposed to pro-inflammatory conditions.

Results

Two unrelated patients with heterozygous deletions of TNFAIP3 manifested complex inflammatory disease. Both inherited the deletion from a healthy parent and expressed the hypomorphic p.I207L allele in trans, inherited from another healthy parent of Oceanian origin. Patient cells demonstrated increased degradation of IkB associated with the compound heterozygote state compared to the deletion alone or p.I207L carrier. Compound heterozygous mice were also more prone to gut and eye inflammation than heterozygous deletion or I207L carriers, in particular when removed from SPF conditions. Polymorphic variants in TNFAIP3 altered A20 phosphorylation and inflammatory response, altering clearance of viruses.

Conclusions

Haploinsufficiency of TNFAIP3 may not always manifest as inflammatory disease, which may require cofactors such as an in trans hypomorphic allele resulting in compound heterozygous inheritance, or a conducive microbial environment. Denisovan I207L appears to have facilitated adaptation to the evolutionary environment of Oceania, but may potentiate the risk of inflammatory disease. This unique genetic variant therefore has Mendelian, population, and species level relevance.